During an upgrade the task: 'Performing Upgrade Task: JRA-34394: Fixing incorrect watch count for cloned issues' caused a re-index error for issues where watchers were added during creation of the issue (using the JIRA Watcher Field Plugin)

The work-around to fix this was to delete the plugin prior to performing the installation.

I'm not sure exactly why this was occurring, but it seemed to be related to this plugin.

Upgraded from 6.3.11 to 6.4.4